Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data

Abstract

Copy number variants (CNVs) play a significant role in human heredity and disease, however sensitive and specific characterization of CNVs from NGS data has remained challenging. Detection is especially problematic for hybridization-capture data in which read counts are the sole source of copy number information. We describe two algorithmic adaptations that improve CNV detection accuracy in a Hidden Markov Model (HMM) context. First, we present a method for com puting target- and copy number state-specific emission distributions. Second, we demonstrate that the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure yields improved sensitivity for small CNV calls compared to the more common Viterbi HMM decoder. We develop a prototype implementation, called Cobalt, and compare it to other CNV detection tools using sets of simulated and previously detected CNVs with sizes spanning a single exon up to a full chromosome. In both the simulation and previously detected CNV studies Cobalt shows similar sensitivity but significantly improved positive predictive value (PPV) compared to other callers. Overall sensitivity is 80%-90% for deletion CNVs spanning 1-4 targets and 90%-100% for larger deletion events, while sensitivity is somewhat lower for small duplication CNVs. Cobalt demonstrates significantly improved positive predictive value (PPV) compared to other callers with similar sensitivity, typically making 5X fewer total calls overall.